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@RoanKanninga RoanKanninga released this 23 Nov 12:55
· 537 commits to master since this release
3.5.1
20e42ea
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Learn about vigilant mode.

MAJOR BUGFIX

MarkDuplicates: lanes from same sample are merged instead of per lane

new:

  • first version of CartegeniaTree (NOT IN USE by diagnostics)

  • Determine trio's (using VCFped, https://github.com/magnusdv/VCFped)

  • using vcfanno for annotation of the variants (https://github.com/brentp/vcfanno/releases) (Field names are between round brackets)

    • CADD (CADD_SCALED, CADD)
    • ExAC (EXAC_AF, EXAC_AC_HET, EXAC_AC_HOM)
    • gnomAD gnomAD_Hom, gnomAD_Hemi, gnomAD_AN, gnomAD_exome_AF_MAX, gnomAD_exome_RF_Filter,EXAC_AF)
    • CGD CGD_Condition, CGD_Inheritance, CGD_AgeGroup, CGD_Manfest_cat, CGD_invent_cat, invent_rat)
    • GoNL (GoNL_AC, GoNL_AN)
    • Clinvar (clinvar_dn, clinvar_isdb, clinvar_hgvs, clinvar_sig)

  • new version of GAVIN (https://github.com/molgenis/gavin-plus/releases)

    • CGD_26jun2018.txt.gz
    • clinvar.vkgl.patho.26june2018.vcf.gz
    • FDR_allGenes_r1.2.tsv
    • GAVIN_calibrations_r0.5.tsv

updated tools

  • SnpEff/4.3t-Java-1.8.0_74
  • multiqc/1.6
  • gavin-plus/1.5.0-Java-1.8.0_74
  • ngs-utils/18.06.2
  • BCFtools/1.6-foss-2015b

new tools:

vcfanno/v0.2.9

updates:

  • created folder that can be picked up by ChronQC for long time statistics
  • removing rejected samples out of samplesheet ( if samples will be rejected this will be mailed to mailing group)
  • added cram index file
  • added single read functionality
  • some data will be moved directly to resultsfolder (bam,cram,fastqc,gVCF)
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